Re: Biology packages in FreeBSD
On Tue, 24 May 2005, Adrian Mastronardi wrote:
A simple comparison shows that below list are not in
debian-med/microbio. It should have some error as ncbi-tools package
exists in debian, probably isn't in debian-med/microbio.
Ahhh, yes. While the ncbi-tools package is in the list of dependencies
of the med-bio meta package it is obviosely missing from the web page.
L-Breeder, ariadne, artemis, avida, babel, biojava, chemeq, coalesce,
crimap, distribfold, dna-qc,
These are really missing (from web pages and also the packages).
embassy,
This is quite connected to Emboss and we have inofficial packages builded
by Matt Hope at
http://debian.bioinformatics.unsw.edu.au/dists/unstable/main/source/science/
see below.
fasta, fasta3,
Here we have probably to do some further investigation: We have the blast2
package which also seems to contain a version of fasta. Could anybody more
educated than me please comment on this?
finchtv, flip, fluctuate, genpak,
Missing.
gff2ps,
Nelson prepared something here. Just have a look at
http://lists.debian.org/debian-med/2005/03/msg00029.html
and the following two mails. IMHO this package might fall in a third
category: "We know that this software exists at this URL, but we will
not package it because ..."
Here the reasons are given in the mails of the thread above: It is just
duplicated functionality with a worse implementation.
I thinks there will be other programs which fall into this category. Tobias,
what do you think about a "grayed out" list?
gperiodic, grappa, kinemage, lamarc,
libgenome, lsysexp, migrate, nab,
Missing.
ncbi-toolkit,
This has just to be added to the web page.
ortep3, p5-AcePerl,
p5-bioperl, paml, povchem, psi88,
Missing.
py24-biopython, py24-martel,
If I'm not completely wrong the python-biopython packages provide exactly
the same code. They are mentioned as BioPython on the web page which is
fine, IMHO. I recently noticed that we have even "competing" Debian packages
for BioPython: The ones builded by Philipp Benner <mail@philipp-benner.de>
(sponsored by me) and the ones in
http://debian.bioinformatics.unsw.edu.au/dists/unstable/main/source/science/
builded by Matt Hope <matth@bioinformatics.unsw.edu.au>. The version from
Philipp is the latest upstream version. This brings up another point:
Matt Hope, who is an official Debian developer maintains a private archive
of biological software. I have heard that the reason for this is that he
has not enough time to bring the packages into a shape which is fit for
official Debian (Matt, please correct me if I'm wrong). My idea would be
to start group maintainance of these packages. If somebody would be able
to offer Matt the help he needs we might quickly be able to move all his
packages to the Debian mirror. I would also spend some time on some of these
packages (perhaps tagging myself as "Uploader" for the packages).
Mat, what are you thinking about this?
recombine, ruby18-bio, seqio, sim4, tRNAscan-SE,
Missing.
treepuzzle,
It's called tree-puzzle in Debian. :)
wise, xmolwt
Missing
xdrawchem
There is a Debian package of it and we just have to discuss, whether this is
a target for med-bio or not.
I'll do a detailed report later tomorrow.
Great job. Thanks, Adrian.
Your comparison has a great value for our project. Moreover I think the existance
of the BSD packages are a big advantage, because we find package descriptions in
the DESC file inside their tbz files and thus we can quickly update our todo list.
Any further comments are welcome
Andreas.
--
http://fam-tille.de
Reply to: